Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcataattgagtagatgtgagtctggattttgagtgtatgtttgtgtagtttttccaccacacatgggttttgattaatcatgtattgggattgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCATTTCGACGTTGCTTAAGGTTGGGATTATTGGTGGGCTTGGTCTCTATGG

Basic information

species Arabidopsis thaliana
transcript AT4G28510.1
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86047136|gb|DR342891.1|DR342891
EST:     CACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCC
genomic: CACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAA-GAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCC
EST: gi|86047137|gb|DR342892.1|DR342892
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047146|gb|DR342901.1|DR342901
EST:     ACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCANAGATACCAGGTGGTGGTGCCA
genomic: ACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047139|gb|DR342894.1|DR342894
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047148|gb|DR342903.1|DR342903
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047134|gb|DR342889.1|DR342889
EST:     TTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: TTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047147|gb|DR342902.1|DR342902
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047144|gb|DR342899.1|DR342899
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047138|gb|DR342893.1|DR342893
EST:     TCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: TCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047143|gb|DR342898.1|DR342898
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047141|gb|DR342896.1|DR342896
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047140|gb|DR342895.1|DR342895
EST:     TTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: TTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047152|gb|DR342907.1|DR342907
EST:     ACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: ACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|125310432|gb|EL324517.1|EL324517
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCTAAAGTTCCTAAAGATACC
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTC-AAAGTTCC-AAAGATACC
EST: gi|86047142|gb|DR342897.1|DR342897
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCYAAGTTCCAAAGATACCANGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047135|gb|DR342890.1|DR342890
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047150|gb|DR342905.1|DR342905
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047145|gb|DR342900.1|DR342900
EST:     CACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047149|gb|DR342904.1|DR342904
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
EST: gi|86047151|gb|DR342906.1|DR342906
EST:     CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAG                         AAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA
genomic: CTCCACGATCTTCCTTTTCCTCTCTCTGCGACTTGAAGCAAAGTTTCCAGgtacgattct ... attgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtttttccaccacacatgggttttgattaatcatgtattgggattgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCATTTCGACGTTGCTTAAGGTTGGGATTATTGGTGGGCTTGGTCTCTATGG
                           gattaat  putative branch site (score: 3)
                                              ttgtttc  putative PPT
                       ttttgattaatcat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcataattgagtagatgtgagtctggattttgagtgtatgtttgtgtagtttttccaccacacatgggttttgattaatcatgtattgggattgtttcagAAAAAGAGATGAACAACGTCAAAGTTCCAAAGATACCAGGTGGTGGTGCCATTTCGACGTTGCTTAAGGTTGGGATTATTGGTGGGCTTGGTCTCTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - -gattttg
- - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttttg